Discovering single nucleotide variants and indels from bulk and single-cell ATAC-seq

Abstract

Genetic variants and de novo mutations in regulatory regions of the genome are typically discovered by whole-genome sequencing (WGS), however WGS is expensive and most WGS reads come from non-regulatory regions. The Assay for Transposase-Accessible Chromatin (ATAC-seq) generates reads from regulatory sequences and could potentially be used as a low-cost 'capture' method for regulatory variant discovery, but its use for this purpose has not been systematically evaluated. Here we apply seven variant callers to bulk and single-cell ATAC-seq data and evaluate their ability to identify single nucleotide variants (SNVs) and insertions/deletions (indels). In addition, we develop an ensemble classifier, VarCA, which combines features from individual variant callers to predict variants. The Genome Analysis Toolkit (GATK) is the best-performing individual caller with precision/recall on a bulk ATAC test dataset of 0.92/0.97 for SNVs and 0.87/0.82 for indels. On bulk ATAC-seq reads, VarCA achieves superior performance with precision/recall of 0.99/0.95 for SNVs and 0.93/0.80 for indels. On single-cell ATAC-seq reads, VarCA attains precision/recall of 0.98/0.94 for SNVs and 0.82/0.82 for indels. In summary, ATAC-seq reads can be used to accurately discover non-coding regulatory variants in the absence of whole-genome sequencing data and our ensemble method, VarCA, has the best overall performance.

Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human Regulatory T cells

“…The development of ATAC-seq has made it possible to quantify chromatin accessibility using a much lower number of cells, therefore making it amenable to the clinical setting and rare cell populations of interest. The measurement of chromatin accessibility at single cell resolution has also become possible with the development of single-cell ATAC sequencing (scATAC-seq) strategies [7][8][9]. In ATAC-seq, Tn5 transposase, preloaded with next-generation sequencing adaptors, simultaneously cuts and ligates sequencing adaptors at accessible open chromatin regions [5,6].…”